Identification of a novel FGFRL1 microRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies
Niu, T and Liu, N and Zhao, M and Xie, G and Zhang, L and Li, J and Pei, YF and Shen, H and Fu, X and He, H and Lu, S and Chen, XD and Tan, LJ and Yang, TL and Guo, Y and Leo, PJ and Duncan, EL and Shen, J and Guo, YF and Nicholson, GC and Prince, RL and Eisman, JA and Jones, G and Sambrook, PN and Hu, X and Das, PM and Tian, Q and Zhu, XZ and Papasian, CJ and Brown, MA and Uitterlinden, AG and Wang, YP and Xiang, S and Deng, HW, Identification of a novel FGFRL1 microRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies, Human Molecular Genetics, 24, (16) pp. 4710-4727. ISSN 0964-6906 (2015) [Refereed Article]
MicroRNAs (miRNAs) are critical post-transcriptional regulators. Based on a previous genome-wide association (GWA) scan, we conducted a polymorphism in microRNAs' Target Sites (poly-miRTS)-centric multistage meta-analysis for lumbar spine (LS)-, total hip (HIP)-, and femoral neck (FN)-bone mineral density (BMD). In stage I, 41,102 poly-miRTSs were meta-analyzed in 7 cohorts with a genome-wide significance (GWS) α = 0.05/41,102 = 1.22 × 10-6. By applying α = 5 × 10-5 (suggestive significance), 11 poly-miRTSs were selected, with FGFRL1 rs4647940 and PRR5 rs3213550 as top signals for FN-BMD (P = 7.67 × 10-6 and 1.58 × 10-5) in gender-combined sample. In stage II in silico replication (two cohorts), FGFRL1 rs4647940 was the only signal marginally replicated for FN-BMD (P = 5.08 × 10-3) at α = 0.10/11 = 9.09 × 10-3. PRR5 rs3213550 was also selected based on biological significance. In stage III de novo genotyping replication (two cohorts), FGFRL1 rs4647940 was the only signal significantly replicated for FN-BMD (P = 7.55 × 10-6) at α = 0.05/2 = 0.025 in gender-combined sample. Aggregating three stages, FGFRL1 rs4647940 was the single stage I-discovered and stages II- and III-replicated signal attaining GWS for FN-BMD (P = 8.87 × 10-12). Dual-luciferase reporter assays demonstrated that FGFRL1 3' untranslated region harboring rs4647940 appears to be hsa-miR-140-5p's target site. In a zebrafish microinjection experiment, dre-miR-140-5p is shown to exert a dramatic impact on craniofacial skeleton formation. Taken together, we provided functional evidence for a novel FGFRL1 poly-miRTS rs4647940 in a previously known 4p16.3 locus, and experimental and clinical genetics studies have shown both FGFRL1 and hsa-miR-140-5p are important for bone formation.